diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetRegistrationHelper.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetRegistrationHelper.java
deleted file mode 100644
index 469e743854bcde173a3ce66dbbeab40aa3edced9..0000000000000000000000000000000000000000
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetRegistrationHelper.java
+++ /dev/null
@@ -1,167 +0,0 @@
-/*
- * Copyright 2010 ETH Zuerich, CISD
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package ch.systemsx.cisd.etlserver.api.v1;
-
-import java.io.File;
-import java.util.concurrent.locks.Lock;
-
-import org.apache.log4j.Logger;
-
-import ch.systemsx.cisd.common.filesystem.FileOperations;
-import ch.systemsx.cisd.common.filesystem.IFileOperations;
-import ch.systemsx.cisd.common.mail.IMailClient;
-import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
-import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
-import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
-import ch.systemsx.cisd.etlserver.IDataStrategyStore;
-import ch.systemsx.cisd.etlserver.IETLServerPlugin;
-import ch.systemsx.cisd.etlserver.IStorageProcessor;
-import ch.systemsx.cisd.etlserver.ITypeExtractor;
-import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
-
-/**
- * @author Chandrasekhar Ramakrishnan
- */
-class DataSetRegistrationHelper extends DataSetRegistrationAlgorithm
-{
-
- private final PutDataSetService service;
-
- private final IETLServerPlugin plugin;
-
- /**
- * @param incomingDataSetFile
- * @param cleanAftrewardsAction
- */
- public DataSetRegistrationHelper(PutDataSetService service, IETLServerPlugin plugin,
- File incomingDataSetFile, IDelegatedActionWithResult<Boolean> cleanAftrewardsAction)
- {
- super(incomingDataSetFile, cleanAftrewardsAction);
- this.service = service;
- this.plugin = plugin;
- }
-
- @Override
- protected IDataSetInfoExtractor getDataSetInfoExtractor()
- {
- return plugin.getDataSetInfoExtractor();
- }
-
- @Override
- protected IDataSetValidator getDataSetValidator()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected String getDataStoreCode()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected IDataStrategyStore getDataStrategyStore()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected String getEmailSubjectTemplate()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected IFileOperations getFileOperations()
- {
- return FileOperations.getMonitoredInstanceForCurrentThread();
- }
-
- @Override
- protected DatabaseInstance getHomeDatabaseInstance()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
- @Override
- protected IMailClient getMailClient()
- {
- return service.getMailClient();
- }
-
- @Override
- protected Logger getNotificationLog()
- {
- return service.getOperationLog();
- }
-
- @Override
- protected IEncapsulatedOpenBISService getOpenBisService()
- {
- return service.getOpenBisService();
- }
-
- @Override
- protected Logger getOperationLog()
- {
- return service.getOperationLog();
- }
-
- @Override
- protected Lock getRegistrationLock()
- {
- return service.getRegistrationLock();
- }
-
- @Override
- protected IStorageProcessor getStorageProcessor()
- {
- return plugin.getStorageProcessor();
- }
-
- @Override
- protected ITypeExtractor getTypeExtractor()
- {
- return plugin.getTypeExtractor();
- }
-
- @Override
- protected void rollback(Throwable ex)
- {
- rollbackStorageProcessor(ex);
- }
-
- @Override
- protected boolean shouldDeleteUnidentified()
- {
- return true;
- }
-
- @Override
- protected boolean shouldNotifySuccessfulRegistration()
- {
- return false;
- }
-
-}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
index 7b4f1d761f4a8eb4338dba929fedc01c394ec41b..9e36df1baca29baa393a2b3ad2e0fc99e1447fcb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
@@ -23,19 +23,33 @@ import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
+import java.util.concurrent.locks.Lock;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.filesystem.FileOperations;
+import ch.systemsx.cisd.common.filesystem.IFileOperations;
import ch.systemsx.cisd.common.io.ConcatenatedFileOutputStreamWriter;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
+import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
+import ch.systemsx.cisd.etlserver.IDataStrategyStore;
import ch.systemsx.cisd.etlserver.IETLServerPlugin;
+import ch.systemsx.cisd.etlserver.IStorageProcessor;
+import ch.systemsx.cisd.etlserver.ITypeExtractor;
+import ch.systemsx.cisd.etlserver.TransferredDataSetHandler;
+import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwner;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO.DataSetOwnerType;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -72,6 +86,10 @@ class PutDataSetExecutor
this.newDataSet = newDataSet;
this.inputStream = inputStream;
this.dataSetDir = new File(service.getIncomingDir(), newDataSet.getDataSetFolderName());
+ if (dataSetDir.exists())
+ {
+ deleteDataSetDir();
+ }
if (false == this.dataSetDir.mkdir())
{
throw new EnvironmentFailureException("Could not create directory for data set "
@@ -94,16 +112,25 @@ class PutDataSetExecutor
writeDataSetToTempDirectory();
- // TODO: When registering, set the registrator to the session owner; only an admin on
- // the space or an ETL server can override.
-
- // Register data set
- DataSetRegistrationHelper helper =
- new DataSetRegistrationHelper(service, plugin, dataSetDir, null);
- helper.prepare();
- helper.registerDataSet();
-
- deleteDataSetDir();
+ // Register the data set
+ try
+ {
+ DataSetRegistrationHelper helper =
+ new DataSetRegistrationHelper(service, plugin, dataSetDir);
+ helper.prepare();
+ if (helper.hasDataSetBeenIdentified())
+ {
+ helper.registerDataSet();
+ } else
+ {
+ helper.dealWithUnidentifiedDataSet();
+ throw new UserFailureException("Could not find owner:\n\t"
+ + newDataSet.getDataSetOwner() + "\nfor data set:\n\t" + newDataSet);
+ }
+ } finally
+ {
+ deleteDataSetDir();
+ }
}
private void writeDataSetToTempDirectory() throws IOException
@@ -114,6 +141,8 @@ class PutDataSetExecutor
{
OutputStream output = getOutputStream(fileInfo);
imagesWriter.writeNextBlock(output);
+ output.flush();
+ output.close();
}
}
@@ -148,24 +177,65 @@ class PutDataSetExecutor
private SpaceIdentifier getSpaceIdentifierForNewDataSet()
{
- SpaceIdentifier spaceId;
+ SpaceIdentifier spaceId = null;
DataSetOwner owner = newDataSet.getDataSetOwner();
- if (DataSetOwnerType.EXPERIMENT == owner.getType())
- {
- ExperimentIdentifier experimentId =
- new ExperimentIdentifierFactory(owner.getIdentifier()).createIdentifier();
- spaceId =
- new SpaceIdentifier(experimentId.getDatabaseInstanceCode(), experimentId
- .getSpaceCode());
- } else
+ switch (owner.getType())
{
- SampleIdentifier sampleId =
- new SampleIdentifierFactory(owner.getIdentifier()).createIdentifier();
- spaceId = sampleId.getSpaceLevel();
+ case EXPERIMENT:
+ {
+ ExperimentIdentifier experimentId = tryExperimentIdentifier();
+ spaceId =
+ new SpaceIdentifier(experimentId.getDatabaseInstanceCode(), experimentId
+ .getSpaceCode());
+ break;
+ }
+ case SAMPLE:
+ {
+ SampleIdentifier sampleId = trySampleIdentifier();
+ spaceId = sampleId.getSpaceLevel();
+ break;
+ }
}
return spaceId;
}
+ private ExperimentIdentifier tryExperimentIdentifier()
+ {
+ DataSetOwner owner = newDataSet.getDataSetOwner();
+ switch (owner.getType())
+ {
+ case EXPERIMENT:
+ {
+ return new ExperimentIdentifierFactory(owner.getIdentifier()).createIdentifier();
+ }
+ case SAMPLE:
+ {
+ return null;
+ }
+ }
+
+ return null;
+ }
+
+ private SampleIdentifier trySampleIdentifier()
+ {
+ DataSetOwner owner = newDataSet.getDataSetOwner();
+ switch (owner.getType())
+ {
+ case EXPERIMENT:
+ {
+ return null;
+ }
+ case SAMPLE:
+ {
+ return new SampleIdentifierFactory(owner.getIdentifier()).createIdentifier();
+
+ }
+ }
+
+ return null;
+ }
+
private IEncapsulatedOpenBISService getOpenBisService()
{
return service.getOpenBisService();
@@ -175,4 +245,175 @@ class PutDataSetExecutor
{
return service.getOperationLog();
}
+
+ private static class CleanAfterwardsAction implements IDelegatedActionWithResult<Boolean>
+ {
+ public Boolean execute()
+ {
+ return true; // do nothing
+ }
+ }
+
+ /**
+ * An implementation of the registration algorithm that gets its state from the executor.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+ private class DataSetRegistrationHelper extends DataSetRegistrationAlgorithm
+ {
+ /**
+ * @param service The provider of global state for the data set registration algorithm
+ * @param plugin The provider of the storage processor
+ * @param incomingDataSetFile The data set to register
+ */
+ public DataSetRegistrationHelper(PutDataSetService service, IETLServerPlugin plugin,
+ File incomingDataSetFile)
+ {
+ super(incomingDataSetFile, new CleanAfterwardsAction());
+ }
+
+ @Override
+ protected IDataSetInfoExtractor getDataSetInfoExtractor()
+ {
+ return plugin.getDataSetInfoExtractor();
+ }
+
+ @Override
+ protected IDataSetValidator getDataSetValidator()
+ {
+ return service.getDataSetValidator();
+ }
+
+ @Override
+ protected String getDataStoreCode()
+ {
+ return service.getDataStoreCode();
+ }
+
+ @Override
+ protected IDataStrategyStore getDataStrategyStore()
+ {
+ return service.getDataStrategyStore();
+ }
+
+ @Override
+ protected String getEmailSubjectTemplate()
+ {
+ return TransferredDataSetHandler.EMAIL_SUBJECT_TEMPLATE;
+ }
+
+ @Override
+ protected IFileOperations getFileOperations()
+ {
+ return FileOperations.getMonitoredInstanceForCurrentThread();
+ }
+
+ @Override
+ protected DatabaseInstance getHomeDatabaseInstance()
+ {
+ return service.getHomeDatabaseInstance();
+ }
+
+ @Override
+ protected IMailClient getMailClient()
+ {
+ return service.getMailClient();
+ }
+
+ @Override
+ protected Logger getNotificationLog()
+ {
+ return service.getOperationLog();
+ }
+
+ @Override
+ protected IEncapsulatedOpenBISService getOpenBisService()
+ {
+ return service.getOpenBisService();
+ }
+
+ @Override
+ protected Logger getOperationLog()
+ {
+ return service.getOperationLog();
+ }
+
+ @Override
+ protected Lock getRegistrationLock()
+ {
+ return service.getRegistrationLock();
+ }
+
+ @Override
+ protected IStorageProcessor getStorageProcessor()
+ {
+ return plugin.getStorageProcessor();
+ }
+
+ @Override
+ protected ITypeExtractor getTypeExtractor()
+ {
+ return plugin.getTypeExtractor();
+ }
+
+ @Override
+ protected void rollback(Throwable ex)
+ {
+ rollbackStorageProcessor(ex);
+ if (ex instanceof UserFailureException)
+ {
+ throw (UserFailureException) ex;
+ }
+ throw new EnvironmentFailureException("Could not register data set " + newDataSet, ex);
+ }
+
+ @Override
+ protected boolean shouldDeleteUnidentified()
+ {
+ return true;
+ }
+
+ @Override
+ protected boolean shouldNotifySuccessfulRegistration()
+ {
+ return false;
+ }
+
+ @Override
+ protected DataSetInformation extractDataSetInformation(final File incomingDataSetPath)
+ {
+ DataSetInformation dataSetInfo = super.extractDataSetInformation(incomingDataSetPath);
+ if (null == dataSetInfo)
+ {
+ return dataSetInfo;
+ }
+ DataSetOwner owner = newDataSet.getDataSetOwner();
+ switch (owner.getType())
+ {
+ case EXPERIMENT:
+ dataSetInfo.setExperimentIdentifier(tryExperimentIdentifier());
+ break;
+ case SAMPLE:
+ SampleIdentifier sampleId = trySampleIdentifier();
+
+ dataSetInfo.setSampleCode(sampleId.getSampleCode());
+ dataSetInfo.setSpaceCode(sampleId.getSpaceLevel().getSpaceCode());
+ dataSetInfo.setInstanceCode(sampleId.getSpaceLevel().getDatabaseInstanceCode());
+ break;
+ }
+
+ // TODO: Get the session owner's email address from OpenBIS
+ // dataSetInfo.setUploadingUserEmail()
+
+ // TODO: When registering, set the registrator to the session owner; only an admin on
+ // the space or an ETL server can override.
+ return dataSetInfo;
+ }
+
+ @Override
+ protected DataSetType extractDataSetType()
+ {
+ return new DataSetType(newDataSet.getDataSetType());
+ }
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
index 849baa5468ef09c71daea18a3005a6c9a91b8379..a5323289a196e44644f740c15cbcffdca8460509 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
@@ -32,8 +32,12 @@ import ch.systemsx.cisd.etlserver.DataStrategyStore;
import ch.systemsx.cisd.etlserver.IETLServerPlugin;
import ch.systemsx.cisd.etlserver.Parameters;
import ch.systemsx.cisd.etlserver.ThreadParameters;
+import ch.systemsx.cisd.etlserver.validation.DataSetValidator;
+import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DssPropertyParametersUtil;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
/**
* Helper class that maintains the state for handling put requests. The requests themselves are
@@ -51,6 +55,12 @@ public class PutDataSetService
private final DataStrategyStore dataStrategyStore;
+ // These are all initialized only once, but it is not possible to initialize them at
+ // construction time, since this causes a dependency loop that causes problems in Spring.
+ private File storeDirectory;
+
+ private String dataStoreCode;
+
private boolean isInitialized = false;
private MailClient mailClient;
@@ -59,6 +69,10 @@ public class PutDataSetService
private File incomingDir;
+ private IDataSetValidator dataSetValidator;
+
+ private DatabaseInstance homeDatabaseInstance;
+
public PutDataSetService(IEncapsulatedOpenBISService openBisService, Logger operationLog)
{
this.openBisService = openBisService;
@@ -80,7 +94,6 @@ public class PutDataSetService
try
{
new PutDataSetExecutor(this, plugin, sessionToken, newDataSet, inputStream).execute();
-
} catch (UserFailureException e)
{
throw new IllegalArgumentException(e);
@@ -108,9 +121,16 @@ public class PutDataSetService
incomingDir.mkdir();
plugin = initializer.getPlugin();
+ plugin.getStorageProcessor().setStoreRootDirectory(storeDirectory);
mailClient = new MailClient(initializer.getMailProperties());
+ this.dataStoreCode = initializer.getDataStoreCode();
+
+ homeDatabaseInstance = openBisService.getHomeDatabaseInstance();
+
+ dataSetValidator = initializer.getDataSetValidator();
+
isInitialized = true;
}
@@ -134,16 +154,41 @@ public class PutDataSetService
return operationLog;
}
- public Lock getRegistrationLock()
+ Lock getRegistrationLock()
{
return registrationLock;
}
- public DataStrategyStore getDataStrategyStore()
+ DataStrategyStore getDataStrategyStore()
{
return dataStrategyStore;
}
+ String getDataStoreCode()
+ {
+ return dataStoreCode;
+ }
+
+ IDataSetValidator getDataSetValidator()
+ {
+ return dataSetValidator;
+ }
+
+ DatabaseInstance getHomeDatabaseInstance()
+ {
+ return homeDatabaseInstance;
+ }
+
+ public File getStoreRootDirectory()
+ {
+ return storeDirectory;
+ }
+
+ public void setStoreDirectory(File storeDirectory)
+ {
+ this.storeDirectory = storeDirectory;
+ }
+
}
/**
@@ -176,4 +221,13 @@ class PutDataSetServiceInitializer
return threadParams[0].getPlugin();
}
+ String getDataStoreCode()
+ {
+ return DssPropertyParametersUtil.getDataStoreCode(params.getProperties());
+ }
+
+ DataSetValidator getDataSetValidator()
+ {
+ return new DataSetValidator(params.getProperties());
+ }
}